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Primary Citation PubMed: 25084326 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 25084326 | PubMedCentral: PMC4118822 | DOI: 10.1107/S1399004714001850

The corresponding structures, solved by molecular replacement with the published structure (Whitney et al. , 2011 ▶ ; PDB entry 3rbh ) as the search model, are referred to herein as AlgE-1.9 (... DB entry 4afk ), AlgE-2.4 (PDB entry 4b61 ) and AlgE-2.8 (PDB entry 4azl ).

The final structures were assessed using MolProbity (Chen et al. , 2010 ▶ ) before deposition into the Protein Data Bank in Europe (PDBe; http://www.ebi.ac.uk/pdbe/ ) with accession codes 4afk (AlgE-1.9), 4azl (AlgE-2.8) and 4b61 (AlgE-2.4).

  AlgE-1.9 (PDB entry 4afk ) AlgE-2.4 (PDB entry 4b61 ) AlgE-2.8 (PDB entry 4azl ) Data collection  Space group C 2 P 2 1 2 1 2 1 P 2 1  Unit-cell parameters    a (Å) 57.25 61.67 47.09    b (Å) 74.42 71.46 245.76    c (Å) 115.53 240.29 47.13   α = γ (°) 90 90 90   β (°) 101.56 90 104.36  Wavelength (Å) 0.97934 0.97934 0.97934  Resolution (Å) 113.18–1.90 (1.97–1.90) 55.64–2.40 (2.53–2.40) 44.90–2.80 (2.95–2.80)   R merge 0.14 (0.35) 0.09 (0.55) 0.22 (0.91)   R r.i.m. 0.15 (0.45) 0.10 (0.58) 0.28 (1.15)  〈 I /σ( I )〉 15.7 (2.9) 6.9 (1.8) 5.8 (2.0)  Completeness (%) 97.7 (84.9) 98.6 (99.9) 93.2 (95.3)  Multiplicity 6.4 (2.5) 9.3 (9.4) 2.7 (2.7)  Wilson B factor (Å 2 ) 15.42 35.72 36.86 Refinement  Resolution (Å) 19.77–1.90 48.87–2.40 44.89–2.80  No.

Supplementary Material PDB reference: AlgE, 4afk PDB reference: 4b61 PDB reference: 4azl Supporting Information.

Publication Year: 2014


A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.

(2015) Acta Crystallogr F Struct Biol Commun 71

PubMed: 25615961 | PubMedCentral: PMC4304740 | DOI: 10.1107/S2053230X14026843

sp Rhodopsin, nonvisual 9.9 MAG 1xio (2.00), 4tl3 (2.30) Channelrhodopsin (1) Chlamydomonas reinhardtii Rhodopsin, nonvisual 9.9 MAG 3ug9 (2.30) Acetabularia rhodopsin II (1) Acetabularia acetabulum R... odopsin, nonvisual 9.9 MAG + cholesterol 3am6 (3.20) Proteorhodopsin (1) Exiguobacterium sibiricum Rhodopsin, nonvisual 9.9 MAG 4hyj (2.30) Light-harvesting complex II (1) Rhodoblastus acidophilus Light-harvesting complex II 9.9 MAG 2fkw (2.45) Cytochrome caa 3 oxidase (1) Thermus thermophilus Cytochrome oxidase 7.7 MAG 2yev (2.36) Prostaglandin E2 synthase 1 (1) Homo sapiens Enzyme 8.8 MAG + DOPC 4bpm (2.08) Na + /Ca + exchanger (1) Methanocaldococcus jannaschii Exchanger 9.9 MAG 3v5u (1.90) Ca 2+ /H + exchanger (VCX1) (1) Saccharomyces cerevisiae Exchanger 9.9 MAG 4k1c (2.30) H + /Ca 2+ exchanger (1) Archaeoglobus fulgidus Exchanger 9.9 MAG 4kpp (2.30) Na + symporter MhsT (1) Bacillus halodurans Symporter 7.8 MAG 4us4 (2.60) Claudin (1) Mus musculus Junction protein 9.9 MAG 4p79 (2.40) GPCRG protein complex (1) Bos taurus , Rattus norvegicus , Homo sapiens G protein-coupled receptorG protein complex 7.7 MAG + cholesterol 3sn6 (3.20) -Barrel AlgE (3) Pseudomonas aeruginosa Transporter 7.8 MAG 4afk (1.90), 4azl (2.80), 4b61 (2.40) OmpF (3) Escherichia coli Channel 9.9 MAG 3poq (1.90), 3pou (2.80), 3pox (2.00) Vitamin B 12 transporter ButB (1) Escherichia coli Transporter 9.9 MAG 2guf (1.95) Adhesin/invasin OpcA (1) Neisseria meningitidis Adhesin 9.9 MAG 2vdf (1.95) Intimin (1) Escherichia coli Adhesin 9.9 MAG 4e1s (1.86) Invasin (1) Yersinia pseudotuberculosis Adhesin 9.9 MAG 4e1t (2.26) -Helix Gramicidin D (4) Brevibacillus brevis Channel 7.7 MAG; 8.8 MAG; 11.7 MAG; 9.9 MAG 2y5m (1.08), 2y6n (1.26), 3zq8 (1.70), 2xdc (1.70)

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4461204

Structure determination and refinement   Molecular replacement (MR) was used to search for a solution in the native lysozyme, PepT St and AlgE data sets using Phaser (McCoy et al. , 2007 ... b6; ) with PDB entries 3tmu (Kmetko et al. , 2011 ▶ ), 4d2b (Lyons et al. , 2014 ▶ ) and 4afk (Tan et al. , 2014 ▶ ) as the model templates, respectively.

The conformation recorded at both temperatures is of the ‘open-in’ type, as reported previously (PDB entry 4afk ; Tan et al. , 2014 ▶ ).

Publication Year: 2015